Dear FSL Developers,
I'm using FLIRT and FNIRT to register each T1 structural image in my dataset to a reference image, the reference image being one of the structural images in my dataset, not a standard template like MNI. The purpose is that I have subject-specific labels – an ROI for a sulci of interest was created for each subject – and I would like to create an average sulci label by combining the subject-specific labels. To summarize, my steps are:
1. flirt, then fnirt each subject to the reference subject
2. apply the warp file from this transform to the subject-specific sulci labels to transform the labels to the reference image
3. combine the warped labels
I read that the -config option in fnirt with $FSLDIR/etc/flirtsch/T1_2_MNI152_2mm.cnf greatly improves the transformation. My question is, is this config file specific to using the MNI152 as the reference image, or would the same config parameters still improve my fnirt if my reference image is a subject in my dataset.
Thanks very much,
Colleen
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